cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b source myp-all2.sh ./mergeMyPar.sh sh-clusters-0hrep1.txt2 ./mergeMyPar.sh sh-clusters-0hrep2.txt2 ./mergeMyPar.sh sh-clusters-0hrep3.txt2 ./mergeMyPar.sh sh-clusters-2hrep1.txt2 ./mergeMyPar.sh sh-clusters-2hrep2.txt2 ./mergeMyPar.sh sh-clusters-2hrep3.txt2 ./mergeMyPar.sh sh-clusters-6hrep1.txt2 ./mergeMyPar.sh sh-clusters-6hrep2.txt2 ./mergeMyPar.sh sh-clusters-6hrep3.txt2 ./mergeMyPar.sh sh-clusters-IGG.txt2 ./mergeMyPar.sh sh-clusters-IL4.txt2 ./mergeMyPar.sh sh-clusters-IFN.txt2 ./mergeMyPar-dist.sh sh-distributions-0hrep1.txt2 ./mergeMyPar-dist.sh sh-distributions-0hrep2.txt2 ./mergeMyPar-dist.sh sh-distributions-0hrep3.txt2 ./mergeMyPar-dist.sh sh-distributions-2hrep1.txt2 ./mergeMyPar-dist.sh sh-distributions-2hrep2.txt2 ./mergeMyPar-dist.sh sh-distributions-2hrep3.txt2 ./mergeMyPar-dist.sh sh-distributions-6hrep1.txt2 ./mergeMyPar-dist.sh sh-distributions-6hrep2.txt2 ./mergeMyPar-dist.sh sh-distributions-6hrep3.txt2 ./mergeMyPar-dist.sh sh-distributions-IGG.txt2 ./mergeMyPar-dist.sh sh-distributions-IL4.txt2 ./mergeMyPar-dist.sh sh-distributions-IFN.txt2 ./mergeMyPar.sh sh-groups-0hrep1.txt2 ./mergeMyPar.sh sh-groups-0hrep2.txt2 ./mergeMyPar.sh sh-groups-0hrep3.txt2 ./mergeMyPar.sh sh-groups-2hrep1.txt2 ./mergeMyPar.sh sh-groups-2hrep2.txt2 ./mergeMyPar.sh sh-groups-2hrep3.txt2 ./mergeMyPar.sh sh-groups-6hrep1.txt2 ./mergeMyPar.sh sh-groups-6hrep2.txt2 ./mergeMyPar.sh sh-groups-6hrep3.txt2 ./mergeMyPar.sh sh-groups-IGG.txt2 ./mergeMyPar.sh sh-groups-IL4.txt2 ./mergeMyPar.sh sh-groups-IFN.txt2 # paralyzer to bed for i in sh-clusters*txt2.csv do echo $i awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2bed.awk $i > $i.bed done #remove IGG regions for i in sh-clusters-*txt2.csv.bed do wc $i bedtools intersect -a $i -b sh-clusters-IGG.txt2.csv.bed -v -s |sort -k1,1 -k2,2n > $i.noIGG wc !$ done 377728 2266368 43311333 sh-clusters-0hrep1.txt2.csv.bed 329388 1976328 37579891 sh-clusters-0hrep1.txt2.csv.bed.noIGG 209599 1257594 23795686 sh-clusters-0hrep2.txt2.csv.bed 183621 1101726 20764309 sh-clusters-0hrep2.txt2.csv.bed.noIGG 560511 3363066 64620965 sh-clusters-0hrep3.txt2.csv.bed 517619 3105714 59456341 sh-clusters-0hrep3.txt2.csv.bed.noIGG 310192 1861152 35376160 sh-clusters-2hrep1.txt2.csv.bed 255706 1534236 28920264 sh-clusters-2hrep1.txt2.csv.bed.noIGG 363384 2180304 41626078 sh-clusters-2hrep2.txt2.csv.bed 325649 1953894 37155450 sh-clusters-2hrep2.txt2.csv.bed.noIGG 361413 2168478 41154576 sh-clusters-2hrep3.txt2.csv.bed 322484 1934904 36572869 sh-clusters-2hrep3.txt2.csv.bed.noIGG 488965 2933790 55438454 sh-clusters-6hrep1.txt2.csv.bed 437198 2623188 49306053 sh-clusters-6hrep1.txt2.csv.bed.noIGG 492195 2953170 56689065 sh-clusters-6hrep2.txt2.csv.bed 440197 2641182 50476786 sh-clusters-6hrep2.txt2.csv.bed.noIGG 231414 1388484 26318939 sh-clusters-6hrep3.txt2.csv.bed 205575 1233450 23294779 sh-clusters-6hrep3.txt2.csv.bed.noIGG 282487 1694922 32048642 sh-clusters-IFN.txt2.csv.bed 245006 1470036 27672878 sh-clusters-IFN.txt2.csv.bed.noIGG 175674 1054044 19813986 sh-clusters-IGG.txt2.csv.bed 0 0 0 sh-clusters-IGG.txt2.csv.bed.noIGG 519579 3117474 59668648 sh-clusters-IL4.txt2.csv.bed 447649 2685894 51025821 sh-clusters-IL4.txt2.csv.bed.noIGG rm sh-clusters-IGG.txt2.csv.bed.noIGG # strand stats for i in sh-clusters-*txt2.csv.bed.noIGG do echo $i awk -f ../strandStats1.awk $i done awk -f ../strandStats1.awk sh-clusters-IGG.txt2.csv.bed sh-clusters-0hrep1.txt2.csv.bed.noIGG nclusters 329388 plus_strand 167695 50.9111 % minus_strand 161693 49.0889 % sh-clusters-0hrep2.txt2.csv.bed.noIGG nclusters 183621 plus_strand 95644 52.0877 % minus_strand 87977 47.9123 % sh-clusters-0hrep3.txt2.csv.bed.noIGG nclusters 517619 plus_strand 265945 51.3785 % minus_strand 251674 48.6215 % sh-clusters-2hrep1.txt2.csv.bed.noIGG nclusters 255706 plus_strand 134920 52.7637 % minus_strand 120786 47.2363 % sh-clusters-2hrep2.txt2.csv.bed.noIGG nclusters 325649 plus_strand 171804 52.7574 % minus_strand 153845 47.2426 % sh-clusters-2hrep3.txt2.csv.bed.noIGG nclusters 322484 plus_strand 162720 50.4583 % minus_strand 159764 49.5417 % sh-clusters-6hrep1.txt2.csv.bed.noIGG nclusters 437198 plus_strand 228504 52.2656 % minus_strand 208694 47.7344 % sh-clusters-6hrep2.txt2.csv.bed.noIGG nclusters 440197 plus_strand 229343 52.1001 % minus_strand 210854 47.8999 % sh-clusters-6hrep3.txt2.csv.bed.noIGG nclusters 205575 plus_strand 111336 54.1583 % minus_strand 94239 45.8417 % sh-clusters-IFN.txt2.csv.bed.noIGG nclusters 245006 plus_strand 129499 52.8554 % minus_strand 115507 47.1446 % sh-clusters-IL4.txt2.csv.bed.noIGG nclusters 447649 plus_strand 229461 51.2591 % minus_strand 218188 48.7409 % IGG nclusters 175674 plus_strand 91102 51.8586 % minus_strand 84572 48.1414 % # separate plus strand results for i in sh-clusters-*txt2.csv.bed.noIGG do wc $i awk -f ../filterPlusStrand.awk $i > $i.plus wc !$ done awk -f ../filterPlusStrand.awk sh-clusters-IGG.txt2.csv.bed > sh-clusters-IGG.txt2.csv.bed.plus 329388 1976328 37579891 sh-clusters-0hrep1.txt2.csv.bed.noIGG 167695 1006170 19198391 sh-clusters-0hrep1.txt2.csv.bed.noIGG.plus 183621 1101726 20764309 sh-clusters-0hrep2.txt2.csv.bed.noIGG 95644 573864 10856011 sh-clusters-0hrep2.txt2.csv.bed.noIGG.plus 517619 3105714 59456341 sh-clusters-0hrep3.txt2.csv.bed.noIGG 265945 1595670 30697937 sh-clusters-0hrep3.txt2.csv.bed.noIGG.plus 255706 1534236 28920264 sh-clusters-2hrep1.txt2.csv.bed.noIGG 134920 809520 15322462 sh-clusters-2hrep1.txt2.csv.bed.noIGG.plus 325649 1953894 37155450 sh-clusters-2hrep2.txt2.csv.bed.noIGG 171804 1030824 19668063 sh-clusters-2hrep2.txt2.csv.bed.noIGG.plus 322484 1934904 36572869 sh-clusters-2hrep3.txt2.csv.bed.noIGG 162720 976320 18496889 sh-clusters-2hrep3.txt2.csv.bed.noIGG.plus 437198 2623188 49306053 sh-clusters-6hrep1.txt2.csv.bed.noIGG 228504 1371024 25918622 sh-clusters-6hrep1.txt2.csv.bed.noIGG.plus 440197 2641182 50476786 sh-clusters-6hrep2.txt2.csv.bed.noIGG 229343 1376058 26389563 sh-clusters-6hrep2.txt2.csv.bed.noIGG.plus 205575 1233450 23294779 sh-clusters-6hrep3.txt2.csv.bed.noIGG 111336 668016 12664508 sh-clusters-6hrep3.txt2.csv.bed.noIGG.plus 245006 1470036 27672878 sh-clusters-IFN.txt2.csv.bed.noIGG 129499 776994 14676834 sh-clusters-IFN.txt2.csv.bed.noIGG.plus 447649 2685894 51025821 sh-clusters-IL4.txt2.csv.bed.noIGG 229461 1376766 26256794 sh-clusters-IL4.txt2.csv.bed.noIGG.plus 329388 1976328 37579891 sh-clusters-0hrep1.txt2.csv.bed.noIGG 183621 1101726 20764309 sh-clusters-0hrep2.txt2.csv.bed.noIGG 517619 3105714 59456341 sh-clusters-0hrep3.txt2.csv.bed.noIGG 255706 1534236 28920264 sh-clusters-2hrep1.txt2.csv.bed.noIGG 325649 1953894 37155450 sh-clusters-2hrep2.txt2.csv.bed.noIGG 322484 1934904 36572869 sh-clusters-2hrep3.txt2.csv.bed.noIGG 437198 2623188 49306053 sh-clusters-6hrep1.txt2.csv.bed.noIGG 440197 2641182 50476786 sh-clusters-6hrep2.txt2.csv.bed.noIGG 205575 1233450 23294779 sh-clusters-6hrep3.txt2.csv.bed.noIGG 245006 1470036 27672878 sh-clusters-IFN.txt2.csv.bed.noIGG 447649 2685894 51025821 sh-clusters-IL4.txt2.csv.bed.noIGG 0 0 0 sh-clusters-*txt2.csv.bed.noIGG 3710092 22260552 422225441 total bash: $i.plus: ambiguous redirect 167695 1006170 19198391 sh-clusters-0hrep1.txt2.csv.bed.noIGG.plus 95644 573864 10856011 sh-clusters-0hrep2.txt2.csv.bed.noIGG.plus 265945 1595670 30697937 sh-clusters-0hrep3.txt2.csv.bed.noIGG.plus 134920 809520 15322462 sh-clusters-2hrep1.txt2.csv.bed.noIGG.plus 171804 1030824 19668063 sh-clusters-2hrep2.txt2.csv.bed.noIGG.plus 162720 976320 18496889 sh-clusters-2hrep3.txt2.csv.bed.noIGG.plus 228504 1371024 25918622 sh-clusters-6hrep1.txt2.csv.bed.noIGG.plus 229343 1376058 26389563 sh-clusters-6hrep2.txt2.csv.bed.noIGG.plus 111336 668016 12664508 sh-clusters-6hrep3.txt2.csv.bed.noIGG.plus 129499 776994 14676834 sh-clusters-IFN.txt2.csv.bed.noIGG.plus 229461 1376766 26256794 sh-clusters-IL4.txt2.csv.bed.noIGG.plus #2 of 3 intersection bedtools multiinter -i sh-clusters-0hrep1.txt2.csv.bed.noIGG.plus sh-clusters-0hrep2.txt2.csv.bed.noIGG.plus sh-clusters-0hrep3.txt2.csv.bed.noIGG.plus > sh-clusters-0h.noIGG.plus.intersection-all.bed bedtools multiinter -i sh-clusters-2hrep1.txt2.csv.bed.noIGG.plus sh-clusters-2hrep2.txt2.csv.bed.noIGG.plus sh-clusters-2hrep3.txt2.csv.bed.noIGG.plus > sh-clusters-2h.noIGG.plus.intersection-all.bed bedtools multiinter -i sh-clusters-6hrep1.txt2.csv.bed.noIGG.plus sh-clusters-6hrep2.txt2.csv.bed.noIGG.plus sh-clusters-6hrep3.txt2.csv.bed.noIGG.plus > sh-clusters-6h.noIGG.plus.intersection-all.bed #bedtools multiinter -i sh-clusters-0hrep1.txt2.csv.bed.noIGG.plus sh-clusters-0hrep2.txt2.csv.bed.noIGG.plus sh-clusters-0hrep3.txt2.csv.bed.noIGG.plus | bedtools merge -i - > foo # sh-clusters-0h.noIGG.plus.intersection-all.bed # merge bed 0610009B22Rik 209 628 ENSMUST00000109098 105 107 2 1,3 1 0 1 0610009B22Rik 209 628 ENSMUST00000109098 107 134 3 1,2,3 1 1 1 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-0h.noIGG.plus.intersection-all.bed | bedtools merge -i - > sh-clusters-0h.noIGG.plus.intersection-all.bed.gt2of3 wc !$ 67712 203136 1921353 sh-clusters-0h.noIGG.plus.intersection-all.bed.gt2of3 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-2h.noIGG.plus.intersection-all.bed | bedtools merge -i - > sh-clusters-2h.noIGG.plus.intersection-all.bed.gt2of3 wc !$ 62194 186582 1763085 sh-clusters-2h.noIGG.plus.intersection-all.bed.gt2of3 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-6h.noIGG.plus.intersection-all.bed | bedtools merge -i - > sh-clusters-6h.noIGG.plus.intersection-all.bed.gt2of3 wc !$ 92673 278019 2623012 sh-clusters-6h.noIGG.plus.intersection-all.bed.gt2of3 awk -v th=2 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-0h.noIGG.plus.intersection-all.bed | bedtools merge -i - > sh-clusters-0h.noIGG.plus.intersection-all.bed.gt3of3 wc !$ 4717 14151 134152 sh-clusters-0h.noIGG.plus.intersection-all.bed.gt3of3 awk -v th=2 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-2h.noIGG.plus.intersection-all.bed | bedtools merge -i - > sh-clusters-2h.noIGG.plus.intersection-all.bed.gt3of3 wc !$ 4895 14685 138725 sh-clusters-2h.noIGG.plus.intersection-all.bed.gt3of3 awk -v th=2 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter-gt-2of3samples.awk sh-clusters-6h.noIGG.plus.intersection-all.bed | bedtools merge -i - > sh-clusters-6h.noIGG.plus.intersection-all.bed.gt3of3 wc !$ 8542 25626 242145 sh-clusters-6h.noIGG.plus.intersection-all.bed.gt3of3 cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/*of3 do echo $i awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1.awk $i |sort -k1,1 -k4,4 -k2,2n -k5,5n > $i.anno.csv # ln -s !$ done awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-clusters-IGG.txt2.csv.bed.plus |sort -k1,1 -k4,4 -k2,2n -k5,5n > sh-clusters-IGG.txt2.csv.bed.plus.anno.csv awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-clusters-IFN.txt2.csv.bed.noIGG.plus |sort -k1,1 -k4,4 -k2,2n -k5,5n > sh-clusters-IFN.txt2.csv.bed.noIGG.plus.anno.csv awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-clusters-IL4.txt2.csv.bed.noIGG.plus |sort -k1,1 -k4,4 -k2,2n -k5,5n > sh-clusters-IL4.txt2.csv.bed.noIGG.plus.anno.csv ( # merge strands for i in sh-clusters-*txt2.csv.bed.noIGG do wc $i cat $i | bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - > $i.unstranded wc !$ done wc sh-clusters-IGG.txt2.csv.bed #88624 531744 9899764 sh-clusters-IGG.txt2.csv.bed cat sh-clusters-IGG.txt2.csv.bed|sort -k1,1 -k2,2n |bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - >sh-clusters-IGG.txt2.csv.bed.unstranded wc sh-clusters-IGG.txt2.csv.bed.unstranded #86814 434070 9671361 sh-clusters-IGG.txt2.csv.bed.unstranded ) #add annotation for i in sh-clusters-*unstranded do echo $i awk -f ../pa2annotate1.awk $i |sort -k1,1 -k2,2n > $i".anno.csv" done # plus strand results cd res/per_sample_plus/ for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/*plus do echo $i awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1.awk $i |sort -k1,1 -k4,4 -k2,2n -k5,5n > $i.anno.csv ln -s !$ done ls s*0h* | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/intersect_modeLocation1.awk > 0h_commonModelocation_GT1.txt ls s*2h* | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/intersect_modeLocation1.awk > 2h_commonModelocation_GT1.txt ls s*6h* | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/intersect_modeLocation1.awk > 6h_commonModelocation_GT1.txt cd ../.. cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/per_sample_plus_sensitive # region stats for i in sh-clusters-*unstranded do echo $i awk -f ../pa2stats1.awk $i done cd res/per_sample/ for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b*anno.csv do ln -s $i done cd ../.. #cluster region union cat sh-clusters-0hrep1.txt2.csv.bed.noIGG.unstranded sh-clusters-0hrep2.txt2.csv.bed.noIGG.unstranded sh-clusters-0hrep3.txt2.csv.bed.noIGG.unstranded| sort -k1,1 -k2,2n | bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - > sh-clusters-0h.noIGG.unstranded.merged.bed 506627 2533135 64580156 sh-clusters-0h.noIGG.unstranded.merged.bed cat sh-clusters-2hrep1.txt2.csv.bed.noIGG.unstranded sh-clusters-2hrep2.txt2.csv.bed.noIGG.unstranded sh-clusters-2hrep3.txt2.csv.bed.noIGG.unstranded| sort -k1,1 -k2,2n | bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - > sh-clusters-2h.noIGG.unstranded.merged.bed 437476 2187380 54900609 sh-clusters-2h.noIGG.unstranded.merged.bed cat sh-clusters-6hrep1.txt2.csv.bed.noIGG.unstranded sh-clusters-6hrep2.txt2.csv.bed.noIGG.unstranded sh-clusters-6hrep3.txt2.csv.bed.noIGG.unstranded| sort -k1,1 -k2,2n | bedtools merge -d -1 -c 4,5 -o collapse,collapse -i - > sh-clusters-6h.noIGG.unstranded.merged.bed 498294 2491470 64601488 sh-clusters-6h.noIGG.unstranded.merged.bed #cluster region intersection bedtools intersect -a sh-clusters-0hrep1.txt2.csv.bed.noIGG.unstranded -b sh-clusters-0hrep2.txt2.csv.bed.noIGG.unstranded -wa -wb -sorted > sh-clusters-0h.noIGG.unstranded.intersection12.bed1 bedtools intersect -a sh-clusters-0hrep3.txt2.csv.bed.noIGG.unstranded -b sh-clusters-0h.noIGG.unstranded.intersection12.bed1 -wa -wb -sorted > sh-clusters-0h.noIGG.unstranded.intersection.bed wc sh-clusters-0h.noIGG.unstranded.intersection.bed 3957 59355 1455714 sh-clusters-0h.noIGG.unstranded.intersection.bed bedtools intersect -a sh-clusters-2hrep1.txt2.csv.bed.noIGG.unstranded -b sh-clusters-2hrep2.txt2.csv.bed.noIGG.unstranded -wa -wb -sorted > sh-clusters-2h.noIGG.unstranded.intersection12.bed1 bedtools intersect -a sh-clusters-2hrep3.txt2.csv.bed.noIGG.unstranded -b sh-clusters-2h.noIGG.unstranded.intersection12.bed1 -wa -wb -sorted > sh-clusters-2h.noIGG.unstranded.intersection.bed wc sh-clusters-2h.noIGG.unstranded.intersection.bed 3851 57765 1400223 sh-clusters-2h.noIGG.unstranded.intersection.bed bedtools intersect -a sh-clusters-6hrep1.txt2.csv.bed.noIGG.unstranded -b sh-clusters-6hrep2.txt2.csv.bed.noIGG.unstranded -wa -wb -sorted > sh-clusters-6h.noIGG.unstranded.intersection12.bed1 bedtools intersect -a sh-clusters-6hrep3.txt2.csv.bed.noIGG.unstranded -b sh-clusters-6h.noIGG.unstranded.intersection12.bed1 -wa -wb -sorted > sh-clusters-6h.noIGG.unstranded.intersection.bed wc sh-clusters-6h.noIGG.unstranded.intersection.bed 6482 97230 2412958 sh-clusters-6h.noIGG.unstranded.intersection.bed